The mitochondrion is the powerhouse of the cell. Therefore, it is critical to the homeostasis of the cell that populations of mitochondria that are damaged or in excess are degraded. The process of targeted elimination of damaged or excess mitochondria by autophagy is called mitophagy. In this report, analysis of the mitophagy regulators PINK1/PARKIN and BNIP3L and their roles are assessed in the lens. PARKIN, an E3 ubiquitin ligase, has been shown to play a role in directing damaged mitochondria for degradation. While BNIP3L, an outer mitochondrial membrane protein, increases in expression in response to excess mitochondria and organelle degradation during cellular differentiation. We have shown that PARKIN is both induced and translocates from the cytoplasm to the mitochondria in human epithelial lens cells upon oxidative stress exposure. In addition, our findings also show that overexpression of BNIP3L causes premature clearance of mitochondria and other organelles, while loss of BNIP3L results in lack of clearance. Prior to this work, PARKIN mediated mitophagy had not been shown to act as a protective cellular response to oxidative stress in the lens. This project also resulted in the novel finding that BNIP3L-mediated mitophagy mechanisms are required for targeted organelle degradation in the lens. / Includes bibliography. / Thesis (M.S.)--Florida Atlantic University, 2015 / FAU Electronic Theses and Dissertations Collection

O aumento da capacidade oxidativa é considerado o fator central dos seus benefícios à saúde induzidos pelo exercício físico aeróbio (EFA). A musculatura esquelética é um dos tecidos mais envolvidos na realização de exercícios físicos, com capacidade notável de adaptação metabólica e estrutural frente ao estímulo mecânico. Os músculos esqueléticos são ricos em mitocôndrias e altamente dependentes da fosforilação oxidativa para a produção energia. Assim, o aumento da capacidade aeróbia induzido pelo EFA ocorre grande parte em função de adaptações mitocondriais. Inúmeros estudos demonstram a capacidade do EFA em induzir biogênese mitocondrial, onde o coativador de transcrição PGC-1?1 atua coordenando a expressão de genes nucleares e mitocondriais no contexto do EFA. No entanto, animais com deleção de PGC- 1?1 no músculo esquelético ainda apresentam remodelamento mitocondrial importante após período de treinamento físico aeróbio, evidenciando a existência de mecanismos ainda desconhecidos. Embora a formação de novas mitocôndrias seja fundamental, a manutenção de mitocôndrias saudáveis por meio de mecanismos de controle de qualidade parece ser de igual ou maior importância para uma adaptação mitocondrial adequada. Um desses mecanismos de controle de qualidade mitocondrial envolve a remoção de mitocôndrias danificadas/envelhecidas via autofagia mitocondrial (mitofagia). Contudo, os mecanismos envolvidos na mitofagia induzida pelo EFA são pouco conhecidos. Considerando o papel da adaptação mitocondrial sobre os efeitos benéficos do EFA, realizamos um estudo exploratório para buscar novos mecanismos envolvidos neste processo. Para isso, utilizamos uma abordagem proteômica direcionada à fração mitocondrial muscular de camundongos submetidos a uma única sessão de EFA. Num primeiro estudo, utilizamos os resultados de proteômica para procurar por proteínas envolvidas na ativação da mitofagia durante o EFA. A partir desse estudo, verificamos que uma sessão de EFA de fato induz sinais de mitofagia na musculatura esquelética. Além disso, propomos que as proteínas Phb2 e Mief2 podem acumular em mitocôndrias danificadas durante o EFA e colaborar para o recrutamento da maquinaria autofágica para a organela, auxiliando no controle de qualidade e adaptação mitocondrial induzidos pelo EFA. Em segundo estudo, tivemos como objetivo identificar nos resultados de proteômica possíveis reguladores de transcrição gênica envolvidos na adaptação mitocondrial induzida pelo EFA. Dessa maneira, identificamos que a proteína mitocondrial Spryd4, cuja função não havia sido estudada até então, parece aumentar na fração mitocondrial muscular durante o EFA. Observamos ainda que a expressão gênica muscular de Spryd4 diminui em camundongos idosos ou com distrofia muscular, aumenta em animais saudáveis após treinamento físico aeróbio e também parece aumentar em humanos treinados. In vitro, observamos que a atenuação da expressão de Spryd4 em miotubos primários promove disfunção mitocondrial, associada à diminuição da expressão de genes de complexos mitocondriais e envolvidos no transporte e metabolismo de lipídeos, além de promover atrofia de miotubos. Num contexto geral, a análise do proteoma mitocondrial muscular após uma sessão de EFA nos permitiu identificar proteínas que parecem estar envolvidas em adaptações mitocondriais, em especial, em mecanismos de mitofagia e controle do fluxo de substratos energéticos / Increased oxidative capacity induced by regular aerobic exercise (AE) is considered a major factor in health. Skeletal muscle is one of the most compromised tissues during exercise and has remarkable metabolic and structural plasticity upon mechanical stimuli. Muscles are rich in mitochondria and heavily reliant on oxidative phosphorylation for energy production. Thus, increased aerobic capacity induced by regular AE occurs largely due to mitochondrial adaptations. Many studies have shown that AE is able to induce mitochondrial biogenesis, and the transcription coactivator PGC-1?1 is known to coordinated gene expression both in nuclei and mitochondria. However, muscle-specific PGC-1?1 knockout mice still display major mitochondrial remodeling after AE training, supporting the existence of unknown mechanisms of AE-induced mitochondrial adaptations. Although making new mitochondria is crucial, the maintenance of a healthy pool of this organelle through mechanisms of quality control seems to be of equal or greater importance during mitochondrial adaptation. One mechanism for mitochondrial quality control comprises the removal of damaged/aged mitochondria via autophagy (mitophagy). Nonetheless, the mechanisms of AE-induced mitophagy are poorly understood. Given the importance of mitochondrial adaptation to the health benefits of AE, we conducted an exploratory study to uncover new mechanisms underlying this process. For this, we performed a proteomic analysis in the skeletal muscle mitochondria-enriched fractions of mice submitted to a single bout of AE. In a first study, we have used these proteomics data to seek for proteins that might be involved in AE-induced mitophagy. On this matter, we confirmed that a single bout of AE in mice increases skeletal muscle mitophagy signaling. Additionally, we suggest that Phb2 and Mief2 accumulate in damaged mitochondria in skeletal muscle during AE and might assist in the recruitment of the autophagic machinery to the organelle, thus aiding to mitochondrial quality control and AE-induced mitochondrial adaptation. In a second study, we have used the same proteomics data to identify transcriptional regulators that might have a role in AE-induced mitochondrial adaptation. Thereby, we have found that the mitochondrial protein Spryd4, whose function was so far unknown, seems to increase in the skeletal muscle mitochondria-enriched fractions following AE. Here we show that skeletal muscle Spryd4 gene expression decreases in aged and dystrophic mice, increases in healthy trained animals and also seems to increase in trained humans. In vitro, we have seen that Spryd4 loss of function in primary myotubes promotes mitochondrial dysfunction, decreases expression of genes involved in mitochondrial complex function, as in fatty acid oxidation and transport. Indeed, Spryd4 loss of function promoted myotube atrophy. Taken together, by analyzing the skeletal muscle mitochondrial proteome after a single bout of AE in mice, we have identified proteins that might participate in AE-induced mitophagy and substrate metabolism, and thus in skeletal muscle adaptation to AE

La peau est un épithélium spécialisé vital et fragile, qui évolue avec l’âge et est influencé par l’environnement, notamment les radiations solaires. Des données sont disponibles sur la réponse du réseau mitochondrial et le devenir des mitochondries endommagées en réponse à des stress chimiques et environnementaux dans plusieurs systèmes expérimentaux, mais ces processus restent peu étudiés dans les cellules cutanées. Dans ce contexte, le projet de thèse visait à analyser l’effet (i) de l’irradiation UVB sur la dynamique mitochondriale (en particulier la fragmentation des mitochondries) dans des kératinocytes primaires humains normaux, qui constituent la première ligne de défense contre les agressions externes ; (ii) d’un traitement par des poisons mitochondriaux sur les mitochondries contenues dans des kératinocytes ou des fibroblastes primaires humains normaux. Dans un premier axe de la thèse, nous avons mis au point une méthode originale (Mitoshape) basée sur l’imagerie confocale, permettant d’estimer à la fois qualitativement et quantitativement la morphologie du réseau mitochondrial dans des cellules vivantes après irradiation UVB. Grâce à cette technologie, nous avons pu montrer que les UVB induisaient une fragmentation du réseau mitochondrial dans les kératinocytes primaires, dont nous avons étudié les acteurs biochimiques. Dans un deuxième axe, nous avons montré que les poisons mitochondriaux avaient la capacité d’endommager les mitochondries dans des kératinocytes et des fibroblastes humains primaires et induisaient une autophagie générale sans toutefois exclure la présence d’une mitophagie dépendante de la voie PINK1/PARKIN. Outre son intérêt fondamental, ce travail (réalisé en collaboration avec la société de cosmétologie SILAB dans le cadre d’un partenariat industriel CIFRE) ouvre la voie à l’identification d’actifs naturels capables de préserver et/ou restaurer les paramètres fonctionnels mitochondriaux suite à des stress. / The skin is a specialized type of epithelium, both vital and fragile, which evolves with age and is continuously exposed to environmental stresses, such as solar radiations. While data is available about the response of the mitochondrial network and the fate of damaged mitochondria after chemical or environmental stresses in numerous experimental systems, little is known about these processes in skin cells. The aim of the present thesis was to study the impact (i) of UVB irradiation on mitochondrial dynamics (especially mitochondrial fragmentation) in normal human epidermal keratinocytes, which represent the first line of defence against environmental insults; (ii) of poisoning mitochondria of keratinocytes and normal human fibroblasts with chemical drugs. In a first axis, we developed an original method (called Mitoshape) based on confocal microscopy, to estimate qualitatively and quantitatively the morphology of the mitochondrial network within live cells following UVB irradiation. Using this technology, we demonstrated that UVB irradiation induces mitochondrial fragmentation in normal human keratinocytes, and studied the biochemical actors involved in this response. In a second axis, we showed that the use of mitochondrial poisons could damage mitochondria of keratinocytes and normal human fibroblasts and induce bulk autophagy, although it is not possible to formally rule out the involvement of a PINK1/PARKIN-dependent pathway of mitophagy. In addition to its fundamental interest, this work (performed in collaboration with the cosmetic company SILAB in the context of a CIFRE PhD fellowship from ANRT) paves the way for the screening of novel bioactive agents able to protect and restore mitochondria following stresses.

Bicarbonato é uma importante espécie química para os seres vivos, sendo o principal tampão celular, alem de apresentar uma negligenciada atividade redox. Isquemia é um evento no qual existe inibição do aporte de nutrientes e oxigênio, sendo a reperfusão o retorno do fluxo de nutrientes e oxigênio, que é acompanhada por alta produção de radicais livres e morte celular. Nessa tese estudamos o efeito da presença de bicarbonato durante a isquemia-reperfusão. Em nosso modelo nós mantivemos o pH constante e modulamos a quantidade de bicarbonato enquanto células, órgãos e animais foram submetidos a isquemia-reperfusão. Utilizamos condições sem a presença de bicarbonato, a concentração basal sanguínea e uma concentração mais alta simulando o acúmulo de bicarbonato em condições isquêmicas. Nesses diversos modelos mostramos que a presença de bicarbonato aumenta o dano provocado por isquemia-reperfusão e provoca um aumento do acúmulo de proteínas oxidadas. A presença do bicarbonato não modifica a respiração, produção de espécies reativas de oxigênio, ou a morfologia mitocondrial, também não detectamos mudança na atividade do proteassoma e nos indicadores de autofagia geral. Entretanto detectamos um acúmulo de marcadores autofágicos na fração mitocondrial indicando inibição da mitofagia. Essa inibição foi confirmada ao detectarmos o acúmulo de uma proteína degradada especificamente por mitofagia enquanto não houve mudança em outra degradada pelo proteassoma. Além disso, ao inibirmos farmacologicamente a autofagia, reproduzimos o fenótipo causado pelo bicarbonato mesmo na sua ausência. Em conclusão, a presença de bicarbonato é deletéria em condições de isquemia/reperfusão devido a inibição da mitofagia / Bicarbonate is an important molecule in all living being, acting as the main cellular buffer. However, its biological and redox activity has been mostly neglected to date. Ischemia is an event in which an inhibition of nutrient availablity and oxygen flow occurs, while reperfusion is the return of nutrients and oxygen, accompanied of a burst of reactive oxygen species production and cell death. Here, we studied the effects of bicarbonate during cardiac ischemia-reperfusion. In our model, we kept the pH stable and changed the concentration of the bicarbonate. We then subjected cells, organs and animals to ischemia-reperfusion under conditions where there was no presence, basal blood concentration or a higher concentration of bicarbonate. In these diverse models, we found that the presence of bicarbonate increased damage after a ischemia-reperfusion, and promoted the accumulation of oxidized proteins. Bicarbonate did not change respiration, production of reactive oxygen species or the morphology of the mitochondria. There were also no changes in proteasome activity and in global autophagy markers, although there was an accumulation of mitophagy markers. We also found that mitophagy was responsible for the increased damage observed, since pharmacological inhibiting of autophagy abolished the increased damage caused by the presence of bicarbonate. In conclusion the presence of bicarbonate is deleterious in ischemia-reperfusion due mitophagy inhibition

Apoptosis is a cell death pathway that regulates tissue homeostasis, and is often altered in oncogenesis. Autophagy is a lysosome degradation pathway that mediates cellular adaptation in response to stresses. Altered autophagy pathways are proposed to be associated with pathogenesis of neurodegenerative diseases and oncogenesis. The goal of this work is to study the complex link between apoptosis and autophagy pathways, and their possible roles in the development of cancer. Using transgenic mice models, we found that impaired apoptosis by overexpression of a dominant negative form of Caspase-9 (Casp9DN) failed to accelerate T-cell lymphoma either by itself or in tumor-prone Bax overexpressing transgenic mice. Additionally, heterozygous disruption of Beclin 1, a central upstream autophagy regulator, failed to promote T-cell lymphoma in either Casp9DN or tumor-prone Bax overexpressing transgenic mice. However, caspase inhibition enhanced a unique form of selective mitochondrial autophagy, referred to as mitochondrial outer membrane permeabilization (MOMP)-induced mitophagy. Parkin, a protein mutated in early-onset Parkinson's disease, mediates mitophagy following protonophore (CCCP) treatment, suggesting that Parkin may also play a role in MOMP-induced mitophagy. Thus, two different types of mitochondrial stresses, MOMP and CCCP, cause mitochondrial depolarization and induce mitophagy. We therefore examined if there is a mechanistic link between two mitophagy pathways. Focusing on the roles of autophagy and apoptosis regulators using isogenic hematopoietic cell lines, our studies demonstrate that MOMP-induced mitophagy is dependent upon Bcl-2 family members, but independent of Parkin or ULK1 (an autophagy regulator). In contrast, CCCP-induced mitophagy is dependent upon Parkin and ULK1, but independent of Bcl-2 family members. However, we found that both pathways ultimately result in the following properties: reduced mitochondrial respiration rate, altered cellular metabolism, and high sensitivity to 2-DG (an inhibitor of glycolysis). Interestingly, 2-DG induced cell death in cells following Parkin-dependent mitophagy is independent of Bcl-2 and Bax/Bak. Overall, the work in this dissertation demonstrates that the two different mitochondrial stresses, MOMP and protonophore (CCCP) treatment, lead to two mechanistically distinct mitophagy pathways, but both alter mitochondrial respiration and cellular metabolism.

La dynamique mitochondriale est impliquée dans la maintenance et la fonction des mitochondries. Dans les graines sèches tout les processus cellulaires sont arrêtés du fait de la faible teneur en eau des tissues, et la transition développementale que représente la germination requiert la réactivation de la dynamique cellulaire. Une approche de bio-imagerie sur la plante modèle Arabidopsis a été utilisée afin d’étudier la réactivation des mitochondries nécessaire à la germination. La réactivation bioénergétique des mitochondries, mesurée par la présence du potentiel membranaire, intervient dès le début de l’hydratation des tissus. Cependant les mitochondries restent statiques et la dynamique mitochondriale ne reprend que plus tardivement. La réactivation des mitochondries provoque une réorganisation du chondriome impliquant la biogenèse de membranes et une fusion massive menant à la formation de structures réticulaires et périnucléaires, qui permet le mélange des nucléoïdes d’ADNmt précédemment isolés en unités discrètes. La mitophagie, un indicateur de la qualité mitochondriale, est réactivée de manière concomitante à la dynamique, alors qu’elle est réprimée durant la biogenèse des mitochondries. La fin de la germination coïncide avec la fragmentation du chondriome tubulaire, menant au doublement du nombre de mitochondrie et à une redistribution hétérogène des nucléoïdes dans le chondriome, générant une population de mitochondrie adaptée à la croissance des plantules. Cette thèse met en évidence l’imbrication des processus de dynamique mitochondriale, de biogenèse et de contrôle qualité des mitochondries requis pour la germination et pour la transition vers l’autotrophie. / Mitochondrial dynamics underpin their function and maintenance. In dry seeds, all cellular processes are in stasis due to a low water content. Thus, the developmental switch leading to germination necessarily involves a reactivation of cellular dynamics. In order tobetter understand the role played by mitochondrial dynamics during germination we used Arabidopsis as a model for a bioimaging approach to investigate the rapid reactivation of mitochondria that is required in order to provide ATP to support germination. Bioenergetic reactivation, visualised as the presence of a mitochondrial membrane potential, is almost immediate upon rehydration. However, the reactivation of mitochondrial dynamics only occurs after several hours of rehydration. The reactivation of mitochondrialbioenergetics and dynamics lead to a dramatic reorganisation of the chondriome involving massive fusion and membrane biogenesis to form a perinuclear tubuloreticular structure enabling mixing of previously discrete mtDNA nucleoids. Mitophagy, an indicator of mitochondrial quality, is reactivated concomitant with a reactivation of mitochondrial dynamics, but is repressed at time of mitochondrial biogenesis. The end of germination coincides with fragmentation of the tubular chondriome leading to a doubling of mitochondrialnumber and heterogeneous redistribution of the nucleoids amongst the mitochondria, generating a population of mitochondria tailored to seedling growth. This thesis provides strong evidence for the tight interweaving of mitochondrial dynamics, mitochondrialbiogenesis and mitochondrial quality control that is required to ensure effective germination and the transition to autotrophy.

La septicémie et les troubles associés demeurent une cause majeure de mortalité dans les unités de soins intensifs. Des récents travaux ont mis en lumière un lien inattendu entre les mitochondries et les fonctions des cellules immunitaires. Des modifications des fonctions mitochondriales ont pu être observées dans les cellules sanguines périphériques lors de septicémies. Dans le cadre de ce travail de thèse, nous avons cherché à évaluer si la mitophagie pouvait avoir un impact sur les fonctions des phagocytes dans le contexte d’une infection bactérienne. La mitophagie est une autophagie dédiée aux mitochondries qui régit l'élimination des mitochondries dysfonctionnelles. Nous avons démontré ici in vivo et in vitro que les macrophages exposés aux bactéries à Gram négatif ou à leurs composants de la paroi cellulaire (Lipopolysaccharides, LPS) présentent une inhibition marquée de la mitophagie qui constitue un mécanisme de protection contre la septicémie. L'activation des macrophages avec une combinaison LPS/IFNγ entraîne une inhibition précoce de la mitophagie dépendante de PINK1 selon une voie dépendante de STAT1-Caspase 11. Cette inhibition de la mitophagie contribue à expliquer la reprogrammation métabolique observée dans les macrophages classiquement activés (macrophages M1) et conduit à une augmentation de la production de ROS mitochondriaux (mROS). En tant que molécules de signalisation, les mROS conduisent à l'activation des macrophages de manière dépendante de HIF-1α et NF-κB. En outre, ces molécules contribuent à la clairance bactérienne dans les phagocytes activés. Il est intéressant de noter que nous avons démontré in vitro et in vivo que la modulation pharmacologique de la mitophagie permet d'imiter ou de réprimer les effets du LPS sur la polarisation des macrophages, la libération des cytokines et l'activité bactéricide. Pour conclure, ce travail démontre que l'inhibition de la mitophagie est une caractéristique de l'activation LPS-dépendante des macrophages et un mécanisme de protection contre les bactéries à Gram négatif. Cette étude souligne également une relation inconnue entre la signalisation IFNγ, les caspases inflammatoires et la mitophagie. Enfin, nos travaux mettent en lumière l'impact des modulateurs pharmacologiques de la mitophagie sur la fonction des macrophages et ouvrent de nouvelles opportunités pour le développement de nouvelles stratégies thérapeutiques pour stimuler la défense de l'hôte. / Sepsis and related organ dysfunctions remain a leading cause of mortality in intensive care units. Increasing evidences have shed light on an unexpected link between mitochondria and immune cell functions. Alterations in mitochondrial functions have been reported in peripheral blood cells in sepsis. We hypothesize here that mitophagy might impact on phagocyte functions in the context of bacterial infection. Mitophagy is a mitochondria-dedicated autophagy that governs the elimination of dysfunctional mitochondria. We demonstrated here in vivo and in vitro that macrophages exposed to Gram-negative bacteria or their cell wall component LPS display a marked inhibition of mitophagy that constitutes a protective mechanism against sepsis. LPS/IFNγ-driven macrophage activation results in early inhibition of PINK1-dependent mitophagy through a STAT1-Caspase 4/11 pathway. This inhibition of mitophagy contributes to explain the metabolic reprogramming observed in classically activated macrophages and leads to a rise in mitochondrial ROS (mROS) production. As signaling molecules, mROS lead to macrophages activation in a HIF-1α- and NF-κB-dependent manner. Furthermore, these molecules contribute to bacterial clearance in activated phagocytes. Interestingly, we demonstrated in vitro and in vivo that pharmacological modulation of mitophagy allows either mimicking or repressing the effects of LPS on macrophages polarization, cytokine release and bactericidal activity. To conclude, this work demonstrates that inhibition of mitophagy is a feature of LPS-dependent macrophage activation and a protective mechanism against Gram-negative bacteria. This study also highlights an unknown relationship between IFNγ-signaling, inflammatory caspases and mitophagy. Finally, our work point out the impact of pharmacological modulators of mitophagy on macrophage function and open new opportunities for the development of novel strategies to boost host defense

<p>Mitochondria are the primary energy producers of the cell and play key roles in cellular signaling, apoptosis and reactive oxygen species (ROS) production. Mitochondria are the only organelles that contain their own genome which encodes for a small subset of electron transport chain (ETC) proteins as well as the necessary tRNAs and ribosomal subunits to translate these proteins. Over 300 pathogenic mitochondrial DNA (mtDNA) mutations have been shown to cause a number of mitochondrial diseases emphasizing the importance of mtDNA maintenance and integrity to human health. Additionally, mitochondrial dysfunction and mtDNA instability are linked to many wide-spread diseases associated with aging including cancer and neurodegeneration. Mitochondria lack the ability to repair certain helix-distorting lesions that are induced at high levels in mtDNA by important environmental genotoxins including polycyclic aromatic hydrocarbons, ultraviolet C radiation (UVC) and mycotoxins. These lesions are irreparable and persistent in the short term, but their long-term fate is unknown. Degradation of mitochondria and mtDNA is carried out by autophagy. Autophagy is protective against cell stress and apoptosis resulting from exposure to mitochondrial toxicants suggesting that it plays an important role in removal of unstable mitochondria that can serve as a source of ROS or initiate apoptotic cell death. Furthermore, dysfunctional mitochondria can be specifically targeted for degradation by the more specific process of mitophagy influenced in part by the processes of mitochondrial dynamics (i.e., fusion and fission). </p><p>The goals of this dissertation were to investigate the long-term fate of helix-distorting mtDNA damage and determine the significance of autophagy and mitochondrial dynamics in removal of and recovery from persistent mtDNA damage. Removal of irreparable mtDNA damage and the necessity of autophagy, mitophagy, fusion and fission genes in removal of this damage were examined using genetic approaches in adult <italic>Caenorhabditis elegans</italic>. In order to investigate the significance of autophagy, fusion and fission genes in recovery from mtDNA damage-induced mitochondrial dysfunction <italic>in vivo</italic>, an experimental method was developed to specifically induce persistent mtDNA damage and mitochondrial dysfunction without persistent nDNA damage in developing <italic>C. elegans</italic>. Additionally, the effect of persistent helix-distorting DNA damage on mitochondrial morphology, mitochondrial function and autophagy was investigated in <italic>C. elegans</italic> and in mammalian cell culture. The rate and specificity of mitochondrial degradation was further examined in cell culture using live-cell fluorescence microscopy and transmission electron microscopy. </p><p>Removal of UVC-induced mtDNA damage was detectable by 72 hours in <italic>C. elegans</italic> and mammalian cell culture, and required mitochondrial fusion, fission and autophagy, providing genetic evidence for a novel mtDNA damage removal pathway. UVC exposure induced autophagy with no detectable effect on mitochondrial morphology in both systems; mitochondrial function was inhibited in the <italic>C. elegans</italic> system but not in the cell culture system in which the degree of mtDNA damage induced was less. Furthermore, mutations in genes involved in these processes as well as pharmacological inhibition of autophagy exacerbated mtDNA damage-mediated larval arrest, illustrating the <italic>in vivo</italic> relevance of removal of persistent mtDNA damage. Mutations in genes in these pathways exist in the human population, demonstrating the potential for important gene-environment interactions affecting mitochondrial health after genotoxin exposure.</p> / Dissertation

Les nucléosides diphosphate kinases (NDPK) sont essentielles pour la génération des nucléosides triphosphates (NTPs) en utilisant l’ATP et des NDPs. L’isoforme mitochondriale de NDPK (NDPK-D), située dans l’espace intermembranaire des mitochondries, possède deux modes de fonctionnement. Dans le premier mode (« phosphotransfert »), la protéine a une activité de kinase comme les autres enzymes NDPK. Dans ce mode de fonctionnement, NDPK-D produit du GTP pour la protéine optique atrophy 1 (OPA1), une GTPase impliquée dans la fusion des mitochondries, et de l’ADP pour le translocateur à adénine (ANT) et l’ATPase mitochondriale pour la régénération d’ATP. Le second mode de fonctionnement est appelé « transfert de lipide » et est lié à la capacité de la protéine à se lier aux phospholipides anioniques, particulièrement la cardiolipine (CL). Dans ce mode NDPK-D peut réticuler les deux membranes mitochondriales et transférer CL de la membrane interne vers la membrane externe des mitochondries, pouvant servir de signal pour la mitophagie et l’apoptose. Ce travail a pour objectif d’étudier plus en détails ces différentes fonctions de NDPK-D. En utilisant des cellules HeLa exprimant de façon stable la protéine sauvage, kinase inactive (mutation H151N) ou incapable de se lier aux lipides (mutation R90D) et des cellules épithéliales de poumons de souris, nous montrons (i) une grande proximité entre NDPK-D et OPA1 qui conduit au channeling de GTP par NDPK-D pour OPA1, (ii) le rôle essentiel de NDPK-D pour l’externalisation de CL vers la surface des mitochondries pendant la mitophagie, servant de signal de reconnaissance pour le complexe LC3-II-autophagosomes afin d’éliminer les mitochondries endommagées, (iii) la possible inhibition de l’externalisation de CL par la présence de complexes NDPK-D/OPA1, et (iv) un phénotype pro-métastatique des cellules HeLa exprimant la NDPK-D mutée (H151N ou R90D), caractérisé par un fort potentiel invasif et migratoire, un profil protéique altéré, et des modifications au niveau structural et fonctionnel du réseau mitochondrial. Finalement, une première stratégie d’expression et de purification de la protéine OPA1 entière a été établie pour de futures études in vitro des complexes NDPK-D/OPA1. / The nucleoside diphosphate kinases (NDPK) are essential for generation of nucleoside triphosphates (NTPs) using ATP and NDPs. The mitochondrial NDPK isoform (NDPK-D) located in the mitochondrial intermembrane space is found to have two modes of function. First, the phosphotransfer mode in which the protein has a kinase activity like other NDPK enzymes. In this mode, NDPK-D produces GTP for the optic atrophy 1 protein (OPA1), a GTPase involved in mitochondrial fusion, and ADP for the adenylate translocator (ANT) and the mitochondrial ATPase for ATP regeneration. The second mode of function is called lipid transfer and is related to the capacity of NDPK-D to bind anionic phospholipids, especially cardiolipin (CL). In this mode, the protein can cross-link the two mitochondrial membranes and transfer CL from the inner to the outer mitochondrial membrane, which can serve as a signal for mitophagy and apoptosis. This work aims to study these NDPK-D functions in more detail. With the use of HeLa cells stably expressing the wild-type, kinase inactive (H151N mutation) or lipid binding deficient (R90D mutation) NDPK-D and mouse lung epithelial cells, we show (i) the close proximity between NDPK-D and OPA1 that leads to GTP channeling from NDPK-D to OPA1, (ii) the essential role of NDPK-D for CL externalization to the mitochondrial surface during mitophagy, serving as a recognition signal for LC3-II-autophagosomes to eliminate damaged mitochondria, (iii) the possible inhibition of CL externalization due to the presence of NDPK-D/OPA1 complexes, and (iv) a pro-metastatic phenotype of HeLa cells expressing either of the NDPK-D mutants (H151N or R90D), characterized by high invasive and migratory potential, altered proteomic profile and changed mitochondrial network structure and function. Finally, a first bacterial expression and purification strategy for full-length OPA1 has been established for future in vitro studies of NDPK-D/OPA1 complexes.

Submitted by Caroline Periotto (carol@ufscar.br) on 2016-09-12T14:10:40Z No. of bitstreams: 1 DissCHM.pdf: 2847929 bytes, checksum: db6163924f9983d42120de5673f3df0a (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-13T14:25:07Z (GMT) No. of bitstreams: 1 DissCHM.pdf: 2847929 bytes, checksum: db6163924f9983d42120de5673f3df0a (MD5) / Approved for entry into archive by Marina Freitas (marinapf@ufscar.br) on 2016-09-13T14:25:18Z (GMT) No. of bitstreams: 1 DissCHM.pdf: 2847929 bytes, checksum: db6163924f9983d42120de5673f3df0a (MD5) / Made available in DSpace on 2016-09-13T14:25:25Z (GMT). No. of bitstreams: 1 DissCHM.pdf: 2847929 bytes, checksum: db6163924f9983d42120de5673f3df0a (MD5) Previous issue date: 2015-11-30 / Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) / Mitochondrial dysfunctions caused by mutations in the mitochondrial DNA (mtDNA) represent an important group of human pathologies. However, it is not possible to predict with accuracy the risk of a woman with mutant mtDNA to transmit her pathology to her descendants. This is mainly due to out limited understanding of the molecular basis of mitochondrial inheritance. Since development of a technology that enabled derivation of induced pluripotent stem cells (iPSCs) from in vitro culture of somatic cells, iPSCs have become an interesting model to study mitochondrial inheritance. Derivation of iPSCs from patients with pathogenic mtDNA mutations has revealed that the mutant load decreases through in vitro culture of iPSCs, suggesting the existence of a specific mechanism that eliminates mutant mtDNA in the germ line. Thus, the aim of this work was to use iPSCs derived from patients with mitochondrial disorders to investigate the existence of a mechanism that eliminates mtDNA molecules with pathogenic mutations. In this way, we used heteroplasmic fibroblasts harboring a point mutation A3243G in mtDNA causing mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS); heteroplasmic fibroblasts harboring a deletion in mtDNA causing Kearn-Sayre Syndrome (KSS) and homoplasmic fibroblasts containing only wild-type mtDNA (Control). The KSS lineage derivation resulted in iPSCs with low levels of mutant mtDNA (<0,1%), and the elimination of mutant molecules during the culture. The MELAS derivation resulted in iPSCs with high levels of mutant mtDNA (> 98%), and indication of mutant molecules elimination as well. However, unexpectedly, there was no reduction of mtDNA content in iPSCs compared to fibroblasts in all lineages. On contrary, mtDNA copy number increased in MELAS and KSS iPSCs, perhaps due to the high levels of mutations in the cells. No effect of Rapamycin (mitophagy inductor) treatment was detected on the yield of colony formation in MELAS iPSCs. Additionally, Rapamycin did not affect the mutation levels in MELAS iPSCS compared to untreated iPSCs. Finally, gene expression analysis of MELAS iPSCs provided evidences of an autophagic mechanism directed towards the mitochondrion. / Disfunções mitocondriais causadas por mutações no DNA mitocondrial (mtDNA) representam um importante grupo de patologias humanas. No entanto, não é possível predizer com acurácia o risco de uma mulher acometida por uma mutação no mtDNA transmitir a patologia para seus descendentes. Isso se deve, em parte, ao desconhecimento dos mecanismos moleculares que controlam a herança mitocondrial. Com o desenvolvimento de metodologias que possibilitam a derivação de células pluripotentes induzidas (iPSCs) a partir de células somáticas cultivadas in vitro, as iPSCs se tornaram um interessante modelo para o estudo da herança mitocondrial. A derivação de iPSCs de pacientes com mutações patogênicas no mtDNA tem revelado que a porcentagem de moléculas mutantes diminui ao longo do cultivo, sugerindo a existência na linhagem germinativa de mecanismos específicos para eliminação de mtDNAs mutantes. Portanto, o presente trabalho investigou em iPSCs derivadas de pacientes com desordens mitocondriais a existência de um mecanismo celular que elimina as moléculas de mtDNA com mutações patogênicas. Para tanto, foram utilizados fibroblastos heteroplásmicos portadores da mutação pontual A3243G no mtDNA causadora de encefalomiopatia mitocondrial, acidose lática e episódios tipo acidente vascular cerebral (MELAS); fibroblastos heteroplásmicos portadores de uma deleção de 4,9 kb no mtDNA causadora da Síndrome de Kearns-Sayre (KSS) e fibroblastos Controle, contendo apenas mtDNA selvagem. A derivação de linhagens portadoras de KSS resultou em iPSCs com baixos níveis de mtDNA mutante (< 0,1%), e na eliminação de moléculas mutantes ao longo do cultivo. A derivação de linhagens portadoras de MELAS resultou em iPSCs com alta taxa de mutação (> 98%), também com indícios de diminuição da quantidade de moléculas mutantes ao longo do cultivo. No entanto, ao contrário do esperado, não houve diminuição da quantidade de cópias de mtDNA nas iPSCs em relação aos fibroblastos em todas as linhagens (Controle, KSS e MELAS), sendo que as iPSCs de MELAS e KSS apresentaram um aumento significativo na quantidade de cópias de mtDNA, provavelmente devido a efeitos causados pela mutação no mtDNA. Ao analisar o efeito do tratamento com Rapamicina (indutor de mitofagia) durante a derivação de MELAS não observamos aumento na eficiência de formação de colônias, além de o tratamento não afetar a quantidade de mtDNA mutante, resultando em iPSCs com níveis de mutação similares aos encontrados nas iPSC MELAS não tratadas com o rapamicina. Por fim, resultados de expressão gênica das iPSCs do grupo MELAS revelaram indícios de mecanismos autofágicos direcionados a mitocôndria provavelmente devido ao efeitos causados pela a alta taxa da mutação. / 2013/13869-5